So far, the recent scandal at a major Jewish charity has focused largely on its leader, Willie Rapfogel. But a new report from Citizens Union makes clear that the politicians and the system that provides taxpayer funding to groups like his scream out for equal scrutiny.

The report is called “Spending in the Shadows,” and it cites $3 billion in “off-budget” cash that will be spent in New York this year via “ ‘lump sum’ pots of money” on the sheer say-so of individual politicians.

It’s a sweet setup for the pols, their pet projects and the groups that get the taxpayer cash. Remember, Rapfogel’s Metropolitan Council on Jewish Poverty got $90 million from all government sources ­last year.

Thanks to secret money “pots,” key budget decisions don’t have to be debated publicly. They can be made after the budget is passed, on the whims of individual officials, and kept from public view. Groups that get cash can then direct donations back to the pols who arranged the funding, just as Rapfogel is thought to have done.

Everyone wins. Except taxpayers.

At $3 billion a year, the sheer amount of this shadow money is alarming enough. But as Citizens Union rightly notes, it raises questions about oversight of the budget process — and the openings for corruption it invites.

Yes, some projects and non-profit work are both vital and legitimate. So why hide their funding from the public or shield it from the budget process?

At least until his trial, we won’t know how much public money, if any, Rapfogel stole and whether he bribed pols to send cash his way. But one thing should already be clear: Secret pots of public dollars guarantee corruption.